Mice with genetically altered expression of costimulatory molecules CD80 (B7-1), CD86 (B7-2), and CD40, or of the costimulatory receptors CD28 and CD154 (CD40 ligand) have been analyzed for thymic development and T cell repertoire. Our findings identify a previously unappreciated role of redundant costimulatory pathways mediating an essential function in thymic development. The effect of these costimulatory pathways on selection of the T cell repertoire was studied in parallel. Two pathways of negative selection have been identified. One pathway is CD40L-dependent and acts at a relatively early stage in intra-thymic development and is mediated by a non-cell-autonomous mechanism. The second is CD40L-independent and occurs later in intra-thymic or post-thymic development. Interestingly, we have observed that when negative selection is abrogated by inactivation of the CD40L pathway, functional self tolerance is maintained by a non-deletional mechanism. This non-deletional tolerance is mediated by a CD28-dependent pathway. Thus, redundant pathways exist to protect against self reactivity in the thymus, and disruption of both C40L (deletional) and CD28 (non-deletional) mechanisms of self tolerance results in a population of highly self-reactive thymic T cells. We have analyzed the signals that mediate T cell-epithelial cell cross-talk during thymic development. We have observed that CD28 costimulation is essential for optimal induction of TNFab in single-positive (SP) thymocytes, and that combined defects in CD40-CD40L and TNFab pathways result in defects in medullary thymic eipthelial cell (mTEC) development that are similar to those in combined CD40-CD40L and CD28-B7 disruption, and are in fact as profound as those seen in complete absence of mature SP TCRab thymocytes. Selective inactivation in TEC of Traf3, an inhibitor of alternative NFkB signaling, restores mTEC development in the complete absence of SP thymocytes and does so through a RelB-dependent pathway. These findings indicate a novel role for CD28-B7 in addition to other mediators of T cell-TEC cross-talk and demonstrate that any and all signals provided by mature thymocytes for mTEC development are provided by activation of RelB-dependent alternative NFkB signaling. The ataxia telangiectasia mutated (ATM) protein plays a central role in sensing and responding to chromatin changes including DNA double strand breaks (dsb) generated by insults such as ionizing radiation. Lymphoid cells are unique in undergoing physiologic dsb in the processes of Ig class switch recombination (CSR) and T or B cell receptor V(D)J recombination, and a role for ATM in these processes has been suggested by clinical observations in ataxia telangiectasia (AT) patients with mutations in the Atm gene as well as by studies of mice deficient in ATM. We characterized a defect in T cell development in ATM-deficient mice that is associated with decreased efficiency in V-J rearrangement of the endogenous T cell receptor (TCR)-alpha locus, with consequent reduction in the number of mature TCR-expressing CD4+ and CD8+ thymic T cells. CD4+CD8+ thymocytes from ATM-deficient mice exhibit a reduction in TCRalpha V-J rearrangement, while containing an increased frequency of unresolved TCR Jbeta coding ends (CE), indicating a delay in TCRalpha V-J coding joint formation. The absence of ATM thus results in reduced frequency of successfully completed TCRalpha recombination, leading to decreased TCRalpha/beta expression and decreased positive selection of mature CD4+ and CD8+ T cells, defining a pivotal role for ATM in T cell development. We have subsequently analyzed the role of ATM in earlier stages of T cell development, including TCR beta rearrangement. In the absence of ATM, VDJ rearrangement of TCRb is defective during the early DN2/3 stage of thymocyte development. This defect has been characterized by direct immuno-FISH visualization of increased DSB foci at the TCRb locus, by decreased productive VDJ recombination, and by decreased expression of TCRb protein. This defect in VDJ recombination reults in functional outcomes that include defective DN3-DN4 and DN-DP developmental transitions, as well as in altered TCRb repertoire as analyzed by deep sequencing of TCRb CD3 regions. These findings thus provide novel insights into the mechanism and functional consequences of ATM during T cell development. Most recently, we have characterized the expression of novel hybrid TCR chains generated by trans-recombination of two distinct TCR loci. Trans recombined genes are expressed at the level of hybrid cell surface receptor chains. Hybrid chains resulting from trans-recombination of TCR gamma variable regions and TCR beta constant regions were identified, and allowed testing of the effect of variable regions on lineage choice (TCR alpha-beta or gamma-delta lineages) and MHC restriction (proposed to be determined by evolutionarily conserved TCR beta V regions). We found that cells expressing these hybrid receptors develop into CD4 and CD8 SP T cells (resembling alpha-beta T cells), undergo MHC-restricted thymic selection despite absence of TCR beta variable region, and support naive and memory mature T cell development. Transgenic mice expressing hybrid receptors have been generated to further define the function of these novel receptors. A central property of the adaptive antigen-specific immune system is the expression by individual T and B lymphocytes of a single antigen receptor, mediating their unique antigen specificity. The expression of only one of the two alleles of a TCR or BCR, known as allelic exclusion, is critical to this process, but the mechanisms mediating allelic exclusion are not fully characterized. In initial experiments, we have found that ATM, best understood as a mediator of DNA damage response, plays a substantial role in TCR beta allelic exclusion. Mature T cells in ATM-deficient mice have an increased proportion of cells expressing two cell surface TCR Vbeta products. Using TCR deep sequencing, measurement of DNA breaks, locus conformation, and the effect of rearranged TCR transgenes, we have made the surprising finding that TCR beta allelic exclusion is intact in ATM-deficient mice during the early DN stage of development at which TCR beta V-D-J rearrangement normally occurs. We have identified a novel mechanism of ATM-dependent locus regulation occurring at later stages of T cell developmental. In the absence of ATM, VDJ recombination continues in the DN4-DP transition, a stage at which rearrangement is normally repressed, leading to bi-allelic TCR beta expression. Generation of the T cell repertoire requires positive selection of cells expressing TCR capable of recognizing foreign antigens, but negatively selected to eliminate cells with potentially dangerous specificity against normal self antigens. The function of costimulatory CD28-B7 and CD40-CD40L pathways in this repertoire selection has not been fully elucidated. We have initiated studies using peptide-MHC tetramers to identify antigen-specific T cells, and have generated the first conditional knockouts for B7 and CD40 to analyze cell type-specific function of these costimulatory pathways in repertoire selection. Generation of the T cell repertoire requires positive selection of cells expressing TCR capable of recognizing foreign antigens, but negatively selected to eliminate cells with potentially dangerous specificity against normal self antigens. The function of costimulatory CD28-B7 and CD40-CD40L pathways in this repertoire selection has not been fully elucidated. We have initiated studies using peptide-MHC tetramers to identify antigen-specific T cells, and have generated the first conditional knockouts for B7 and CD40 to analyze cell type-specific function of these costimulatory pathways in repertoire selection.